| Tuesday 17th July 2012 | |||
| 1st Leg | |||
| F91 Dudelange | 1-0 | Salzburg | |
| Flora Tallinn | 0-2 | Basel | |
| HJK Helsinki | 7-0 | KR Reykjavik | |
| MSK Zilina | 1-0 | Hapoel Ironi KS | |
| Neftchi Baku | 3-0 | Zestafoni | |
| Shamrock Rovers | 0-0 | FK Ekranas Panevezys | |
| Skenderbeu | 1-0 | Debreceni VSC | |
| Slovan Liberec | 1-0 | Shakhtar Donetsk | |
| The New Saints | 0-0 | Helsingborgs | |
| Ulysses Yerevan | 0-1 | Sheriff Tiraspol | |
| Valletta | 1-4 | Partizan Belgrade | |
| Wednesday 18th July 2012 | |||
| 1st Leg | |||
| AEL Limassol | 3-0 | Linfield | |
| BATE Borisov | 3-2 | FK Vardar Skopje | |
| Buducnost Podgorica | 0-2 | Slask Wroclaw | |
| Ludogorets Razgrad | 1-1 | Dinamo Zagreb | |
| Molde | 3-0 | FK Ventspils | |
| NK Maribor | 4-1 | Zeljeznicar Sarajevo | |
| Tuesday 24th July 2012 | |||
| 2nd Leg | |||
| Basel | 3-0 | Flora Tallinn | (5-0) |
| Debreceni VSC | 3-0 | Skenderbeu | (3-1) |
| FK Ekranas Panevezys | 2-1 | Shamrock Rovers | (2-1) |
| FK Ventspils | 1-1 | Molde | (1-4) |
| Hapoel Ironi KS | 2-0 | MSK Zilina | (2-1) |
| KR Reykjavik | 1-2 | HJK Helsinki | (1-9) |
| Partizan Belgrade | 3-1 | Valletta | (7-2) |
| Salzburg | 4-3 | F91 Dudelange | (4-4) |
| (F91 Dudelange won on away goals) | |||
| Shakhtar Donetsk | 1-1 | Slovan Liberec | aet (1-2) |
| Sheriff Tiraspol | 1-0 | Ulysses Yerevan | (2-0) |
| Zeljeznicar Sarajevo | 1-2 | NK Maribor | (2-6) |
| Zestafoni | 2-2 | Neftchi Baku | (2-5) |
| Wednesday 25th July 2012 | |||
| 2nd Leg | |||
| Dinamo Zagreb | 3-2 | Ludogorets Razgrad | (4-3) |
| FK Vardar Skopje | 0-0 | BATE Borisov | (2-3) |
| Helsingborgs | 3-0 | The New Saints | (3-0) |
| Linfield | 0-0 | AEL Limassol | (0-3) |
| Slask Wroclaw | 0-1 | Buducnost Podgorica | (2-1) |
